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Created by fconstancias@fconstancias

Error in rule CTDT:

Dear PathoFact developers,

Thanks for your effort developping this very usefull tool.

Could you clarify the different branches (orf_coinf, orf, PathoFact_v, master ...) ?

I am using PathoFact using already annotated contigs i.e., ORFs https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf_coinf and I prepared the necessary files: .fna .faa .contig using the script: https://raw.githubusercontent.com/fconstancias/NRP72-FBT/master/functions/prepare_faa_fna_PAthoFact_orf.Rscript.R

I am using the enclosed config.yaml

I run the pipeline using snakemake -s Snakefile --use-conda --reason --cores 10 -p --configfile analyses/config.yaml

everything went smooth until the following error:

[Fri Jul  1 16:05:57 2022]
Finished job 321.
277 of 1075 steps (26%) done

[Fri Jul  1 16:05:57 2022]
Job 324: Identify features (CTDT) on the following sample(s): PathoFact_results - chicken1_l10000
Reason: Missing output files: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_22_CTDT.txt

python scripts/CTDT.py --file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/splitted/chicken1_l10000/group_22.fasta --out /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_22_CTDT.txt &> /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_22_CTDT.log
Activating conda environment: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
Activating conda environment: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
[Fri Jul  1 16:05:59 2022]
Error in rule CTDT:
    jobid: 319
    output: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_6_CTDT.txt
    log: /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_6_CTDT.log (check log file(s) for error message)
    conda-env: /datadrive05/Flo/tools/orf_coinf/.snakemake/conda/67994cc8
    shell:
        python scripts/CTDT.py --file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/splitted/chicken1_l10000/group_6.fasta --out /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_6_CTDT.txt &> /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/logs/chicken1_l10000/group_6_CTDT.log
        (exited with non-zero exit code)

Removing temporary output file /datadrive05/Flo/tools/orf_coinf/analyses/PathoFact_results/PathoFact_intermediate/VIRULENCE/classifier_virulence/chicken1_l10000/group_49_matrix.tsv.
[Fri Jul  1 16:06:00 2022]
Finished job 66.

Please find enclosed the logs: 2022-07-01T155547.324708.snakemake.log group_6_CTDT.log as well as the group_6.fasta.gz

conda --version
conda 4.12.0

environment.yml

It seems specific to the VIR workflow since AMR and Tox worked fine on the same dataset. Thanks for the support!

Edited by fconstancias